- "Marcus used me to design weapons to help him realize his vision of a militarized Starfleet. He sent you to use those weapons, to fire my torpedoes on an unsuspecting planet, and then he purposely crippled your ship in enemy space, leading to one inevitable outcome: the Klingons would come searching for whomever was responsible, and you would have no chance of escape. Marcus would finally have the war he talked about, the war he always wanted."
- — Khan Noonien Singh
The militarization conspiracy was a plot by Section 31 to militarize Starfleet in the wake of the destruction of Vulcan to prepare for war against the Klingon Empire. Admiral Alexander Marcus sought this by utilizing the intellect of the revived war criminal Khan Noonien Singh. When this backfired with tragic results, Marcus went to extreme lengths to cover up the conspiracy all while exploiting opportunities to begin his war.
History[]
Origins[]
- "I took a tactical risk when I woke that bastard up, believing that a superior intelligence could help us protect ourselves from whatever came at us next. But I made a mistake, and now the blood of everyone he's killed is on my hands."
- — Alexander Marcus, 2259
Following the destruction of the USS Kelvin in 2233, the USS Enterprise under Captain Robert April and his XO, Alexander Marcus conducted a survey of the planet Phaedus IV around 2239. There, April witnessed a civil war between the Phaedans and saw the atrocities carried out by the Shadow. Thus, April decided to violate the Prime Directive and assist the blue Phaedans. April then took some technology and Marcus reported that April had been killed. For the next twenty years, April and the blue Phaedans fought the Shadow with supplies from Section 31 sent through the smuggler Mudd. April then discovered that the Shadow were being backed by the Klingon Empire.
April and Mudd Incident[]
Following the Gorn's attempted invasion, the Enterprise under Captain James T. Kirk was ordered by Admiral Christopher Pike to do a survey on Nibiru. However, Admiral Marcus had the Enterprise do another survey at Phaedus IV. Once there, the Enterprise detected a high frequency energy field coming from the planet. Kirk took a landing party to investigate the energy field. As they made their approach, Kirk's shuttle came under fire from the natives and was forced to crash land on the surface.
Kirk and Spock were then found by a group of Phaedans equipped with starfleet equipment and a Universal translator. Kirk asked where they got the equipment and Captain April revealed himself to Kirk. April, lying about Sulu and Hendorff's location, took Kirk and Spock into a cave protected by holographic camouflage. April revealed that he chose to stay behind in order to protect the Phaedans from the Shadows' attrocities by violating the prime directive. He also revealed that Marcus, when he was the USS Enterprise's XO, faked his death, stayed in contact with him and supplied technology to him through Section 31 and the smuggler Mudd. Spock was able to rescue Sulu and Hendorff from the Shadow and discovered that the Klingon Empire were backing the shadow with weapons.
April, using Protocol 31, was able to take control of the Enterprise. He then contacted Commander Kor and offered him the Enterprise in exchange for the governorship of Phaedus. However, Scott was able disable the protocol and enable Kirk to take the Enterprise back from April and leave Phaedus. Kirk was then ordered to leave April at the next starbase.
Marcus and Section 31's plans[]
When Marcus became the head of Starfleet in the 2250s decade, he was dissatisfied with the Federation's response to the Klingon Empire's belligerent expansion. Believing war with the Klingons was inevitable, Marcus and a Section 31 faction sought ways to militarize Starfleet. Following the destruction of Vulcan in 2258, the USS Vanguard discovered the SS Botany Bay, that had 73 Augment Humans from the late 20th century Earth. Marcus woke the Augments' leader, Khan Noonien Singh. Marcus then had Khan surgically altered recruited him into Section 31 under the alias "John Harrison".
Khan's revenge[]
- "I had no choice but to escape alone. And when I did, I had every reason to suspect that Marcus had killed every single one of the people I hold most dear. So I responded in kind."
- — Khan Noonien Singh, 2259

The bombing in London
Believing that Marcus had made good on his threat to kill Khan's crew, Khan plotted revenge on Starfleet. He approached Section 31 officer Thomas Harewood, whose daughter was terminally ill, and offered to save her life if Harewood would destroy a Section 31 facility in London. After Khan fulfilled his part of the bargain, Harewood did likewise by detonating a bomb disguised as his Starfleet Academy ring, killing himself and 41 others. In the ensuing chaos, Khan salvaged a portable transwarp beaming device from the rubble.
The bombing mandated a meeting of Starfleet's senior leadership at the Daystrom Conference Room in Starfleet Headquarters, where Marcus declared a manhunt for "Harrison". Having anticipated just such a meeting, Khan commandeered jumpship 208 and attacked, killing Christopher Pike and several other officers before he was forced to withdraw by James T. Kirk. Khan escaped via transwarp beaming to the uninhabited Ketha Province of Qo'noS, where Starfleet ostensibly could not follow.
Path to war[]
- "That's what scares me: This is clearly a military operation. Is that what we are now? 'Cause I thought we were explorers."
- — Montgomery Scott, 2259
Devastated by Pike's death, Kirk implored Marcus to authorize an off-the-book mission to pursue Harrison. Marcus saw in Kirk the opportunity to eliminate Khan, cover up his conspiracy, and incite war with the Klingons on his terms, all in a single stroke. Marcus instructed Kirk to take the USS Enterprise to the Klingon Neutral Zone and kill Harrison using 72 long-range torpedoes, which he knew contained Khan's crew. He also arranged for the sabotage of the Enterprise's warp core, which would leave her stranded when the Klingons came to investigate the source of the torpedoes; war would undoubtedly follow.
Enterprise first officer Spock strongly objected to executing Harrison without trial, and ultimately prevailed on Kirk to arrest Harrison instead. Despite the failure of the Enterprise's warp drive, Kirk decided to proceed with the mission. On the surface of Qo'noS, the Enterprise away team ran afoul of a Klingon patrol, who were in turn slaughtered by Harrison. Harrison then surrendered himself, inferring correctly that his crew was still alive from the presence of the torpedoes on the Enterprise. Kirk sent a message to Starfleet informing them that he had Harrison in custody, inadvertently alerting Marcus that he was in danger of being exposed.
Aboard the Enterprise, Harrison revealed his true identity and his involvement with Marcus. At his urging, Leonard McCoy and Carol Marcus opened a torpedo and found one of Khan's crew inside. Khan also gave Kirk the coordinates of the Io Facility, which Kirk passed to Montgomery Scott on Earth. Scott arrived at the drydock as the Vengeance was preparing to launch, and sneaked aboard.
Battle over Luna[]
- "War is coming – and who's gonna lead us? You?! If I'm not in charge, our entire way of life is decimated!."
- — Alexander Marcus, 2259
The Vengeance arrives
Marcus, commanding the Vengeance, confronted the Enterprise at the edge of Klingon space and ordered Kirk to hand over Harrison, to which Kirk demurred. After Kirk revealed his knowledge of Khan's crew, Marcus concluded that everyone on the Enterprise needed to be silenced.

The Vengeance fires on the Enterprise
The Enterprise raced for Earth, bringing evidence of Marcus's conspiracy. However, the technologically superior Vengeance overtook the Enterprise and forced her out of warp near Luna with a phaser barrage, 237,000 kilometers short of Earth. Marcus rejected Kirk's plea for mercy and prepared to destroy the Enterprise, only to find the Vengeance's systems disrupted from within by Scott. The temporary lull allowed Kirk and Khan to board the Vengeance in environmental suits.
Kirk, Scott, and Khan made their way to the Vengeance bridge and seized control, though Marcus remained defiant. Khan promptly turned against Kirk, overwhelmed his team, and murdered Marcus. He then demanded that Spock surrender his crew or face destruction. Spock complied, allowing Khan to transport the 72 torpedoes to the Vengeance in exchange for Kirk and the others. Khan opened fire on the Enterprise, unaware that Spock had foreseen his treachery and armed the torpedoes, after McCoy removed the cryo-tubes. The explosion of the torpedoes crippled the Vengeance.

The Enterprise plummeting to Earth
The two starships, both critically damaged, were caught by Earth's gravity and began falling toward the surface. Kirk managed to reactivate the Enterprise's warp core in time to avert a crash, suffering fatal radiation poisoning in the process. Khan, believing his crew dead, directed the Vengeance to crash into Starfleet Headquarters in a final act of spite. The enormous ship plowed through San Francisco, obliterating landmarks like Alcatraz Penitentiary and killing many civilians before coming to a rest.
Khan survived the crash and leaped from the wreck in a bid for freedom. Spock pursued him with the intent of killing him to avenge Kirk's death. The two fought, though Khan eventually gained the upper hand. Meanwhile, McCoy realized that Khan's blood could be used to revive Kirk. Nyota Uhura beamed down and stunned Khan repeatedly, allowing Spock to defeat and incapacitate him.
Aftermath[]
- "When Christopher Pike first gave me his ship, he had me recite the Captain's Oath, words I didn't appreciate at the time. Now I see them as a call for us to remember who we once were, and who we must be again."
- — James T. Kirk, 2260

Vengeance comes to San Francisco
McCoy performed a blood transfusion to restore Kirk to life. Khan was placed back into stasis with the rest of his crew.
Nearly a year later, Kirk spoke at a memorial for the lives lost as a result of Khan and Admiral Marcus' actions. In his speech, Kirk reminded the attendees that Starfleet's true mission was the exploration of the galaxy. Shortly afterward, he returned to the Enterprise, to begin the first five-year mission.
The conspiracy ultimately failed since, as Montgomery Scott once stated, Starfleet was not a military organization.
Despite Starfleet's efforts, Section 31 continued with operations against both the Klingons and the Romulan Empire. They provided the Romulan warbirds under Commander L'Nar with weaponry based on the Vengeance's systems.